Rw5G026650

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0000025
Physical Location & Seq
Forward (+)
38645896 .. 38648449
2554 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G026650.1

Sequence Viewer

Length: 363 bp
ATGAGAACACTCTTTGGGGGGGGTCAGAGTGTAGTGTGGTATTTGTCCGTCTCTGGGTTTTGGAGCTCTTGGAAAGTTGGCACAATGAAGATCAAGGAAGAGAAGGAAGATGTATCCGACACATTCATATGGAAAGTCCGCTTATCTGAGCTCAAGAACAGCCGAAATTGCTCTGACACTTCCACCGTCGGTGGTCTTAAATGGCACATTATTGCATGTCCAAGGTTATGTGATGAAAATTCCTGTGGAGCAGTTATCATGTACTTGGCTGTTGCAGATGCTTCAGGATTGCCAGTTGGGTGGAGTAGACTTGCTCGCCCTACCTTTCCTTGGTTAATCAACTTGACAGCAAGAAGTCAATAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
Retrotran_gag_2 gag_pre-integrs zf-CCHC

Protein Analysis

120

Amino Acids

13.4

Weight (kDa)

9.04

Isoelectric Point (pI)

48.7

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
MATH_2 PF22486 41 - 109 3.4e-06 MATH domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000025)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G31370 AT1G31380 AT1G31390 AT1G31400 AT2G01790 AT2G05400 AT2G05400 AT2G05400 AT2G05410 AT2G05410 AT2G05420 AT2G05430 AT2G42455 AT2G42460 AT2G42465 AT2G42470 AT2G42475 AT2G42480 AT3G27040 AT3G29580 AT3G44790 AT3G44800 AT3G44805 AT3G58200 AT3G58210 AT3G58220 AT3G58220 AT3G58220 AT3G58220 AT3G58220 AT3G58230 AT3G58240 AT3G58250 AT3G58260 AT3G58270 AT3G58270 AT3G58270 AT3G58280 AT3G58290 AT3G58290 AT3G58290 AT3G58300 AT3G58320 AT3G58330 AT3G58340 AT3G58340 AT3G58350 AT3G58350 AT3G58360 AT3G58370 AT3G58380 AT3G58400 AT3G58410 AT3G58410 AT3G58430 AT3G58430 AT3G58440 AT5G03550
fragaria_vesca FvH4_2g00084 FvH4_2g15701 FvH4_2g24334 FvH4_3g23322 FvH4_3g23322 FvH4_3g23322 FvH4_3g23482 FvH4_3g23482 FvH4_3g23482 FvH4_3g23491 FvH4_3g23492 FvH4_3g23510 FvH4_3g23520 FvH4_3g23520 FvH4_3g23520 FvH4_3g23580 FvH4_3g38842 FvH4_4g10396 FvH4_5g29370 FvH4_5g32130 FvH4_7g04570 FvH4_7g04571 FvH4_7g04741 FvH4_7g04741 FvH4_7g04750 FvH4_7g04750 FvH4_7g04760 FvH4_7g04760 FvH4_7g04760 FvH4_7g04760 FvH4_7g04760 FvH4_7g04770 FvH4_7g04770 FvH4_7g04770
malus_domestica MD00G1065000.v1.1 MD00G1065300.v1.1 MD02G1267400.v1.1 MD02G1267600.v1.1 MD02G1267700.v1.1 MD02G1267800.v1.1 MD02G1268100.v1.1 MD02G1268300.v1.1 MD02G1268400.v1.1 MD02G1268500.v1.1 MD03G1193600.v1.1 MD05G1071400.v1.1 MD07G1051000.v1.1 MD07G1051100.v1.1 MD07G1051200.v1.1 MD07G1051300.v1.1 MD07G1051500.v1.1 MD07G1051700.v1.1 MD07G1051800.v1.1 MD07G1085400.v1.1 MD07G1085500.v1.1 MD11G1177200.v1.1 MD11G1209800.v1.1 MD11G1209900.v1.1 MD11G1210000.v1.1 MD12G1048100.v1.1 MD12G1048600.v1.1 MD14G1046700.v1.1 MD14G1047400.v1.1
prunus_persica Prupe.2G051200_v2.0.a1 Prupe.2G052500_v2.0.a1 Prupe.2G052500_v2.0.a1 Prupe.2G052600_v2.0.a1 Prupe.2G052600_v2.0.a1 Prupe.2G052700_v2.0.a1 Prupe.2G052800_v2.0.a1 Prupe.2G052900_v2.0.a1 Prupe.2G052900_v2.0.a1 Prupe.2G053100_v2.0.a1 Prupe.2G053300_v2.0.a1 Prupe.2G054800_v2.0.a1 Prupe.2G054900_v2.0.a1 Prupe.2G054900_v2.0.a1 Prupe.2G054900_v2.0.a1 Prupe.2G069300_v2.0.a1 Prupe.2G069300_v2.0.a1 Prupe.2G069300_v2.0.a1 Prupe.2G069300_v2.0.a1 Prupe.2G069300_v2.0.a1 Prupe.4G223300_v2.0.a1 Prupe.4G223300_v2.0.a1
pyrus_communis pycom01g04720 pycom02g22950 pycom02g22960 pycom02g22970 pycom02g22990 pycom02g23000 pycom02g23010 pycom03g14600 pycom03g14610 pycom05g06150 pycom07g03820 pycom07g03830 pycom07g03850 pycom07g03860 pycom07g03880 pycom07g03890 pycom07g03900 pycom07g04000 pycom07g04010 pycom11g18540 pycom11g18560 pycom12g04190 pycom17g19100
rosa_chinensis RchiOBHm_Chr0c19g0500051 RchiOBHm_Chr1g0330011 RchiOBHm_Chr1g0330031 RchiOBHm_Chr1g0330041 RchiOBHm_Chr1g0330121 RchiOBHm_Chr1g0330141 RchiOBHm_Chr1g0330151 RchiOBHm_Chr1g0330181 RchiOBHm_Chr1g0330191 RchiOBHm_Chr1g0330201 RchiOBHm_Chr1g0330211 RchiOBHm_Chr1g0330221 RchiOBHm_Chr1g0367471 RchiOBHm_Chr2g0113311 RchiOBHm_Chr2g0148281 RchiOBHm_Chr4g0400061 RchiOBHm_Chr4g0437571 RchiOBHm_Chr5g0041361 RchiOBHm_Chr5g0041421 RchiOBHm_Chr5g0041481 RchiOBHm_Chr5g0041491 RchiOBHm_Chr5g0041501 RchiOBHm_Chr5g0041511 RchiOBHm_Chr5g0042491 RchiOBHm_Chr5g0042501 RchiOBHm_Chr6g0263551 RchiOBHm_Chr6g0286221 RchiOBHm_Chr7g0228171 RchiOBHm_Chr7g0231391 RchiOBHm_Chr7g0231401
rosa_laevigata RLG00000000870 RLG00000001420 RLG00000001582 RLG00000001602 RLG00000001700 RLG00000002476 RLG00000005787 RLG00000007689 RLG00000008446 RLG00000008811 RLG00000008812 RLG00000009013 RLG00000009942 RLG00000012752 RLG00000013511 RLG00000014053 RLG00000015257 RLG00000015258 RLG00000016149 RLG00000016691 RLG00000018661 RLG00000018662 RLG00000020991 RLG00000020992 RLG00000020993 RLG00000027309 RLG00000028568 RLG00000029119 RLG00000029371 RLG00000029563 RLG00000029818 RLG00000029819 RLG00000029821 RLG00000029822 RLG00000029824 RLG00000029827 RLG00000029828 RLG00000029829 RLG00000029841 RLG00000029843 RLG00000032676 RLG00000033366 RLG00000033367 RLG00000034023 RLG00000034066 RLG00000034072 RLG00000034073 RLG00000034074 RLG00000034130 RLG00000034133 RLG00000035487 RLG00000035488 RLG00000035793
rosa_multiflora Rmu_co8241405.1_g000001 Rmu_co8251033.1_g000001 Rmu_co8297611.1_g000001 Rmu_co8346639.1_g000001 Rmu_co8405917.1_g000001 Rmu_sc0000045.1_g000044 Rmu_sc0000061.1_g000032 Rmu_sc0000068.1_g000021 Rmu_sc0000068.1_g000022 Rmu_sc0000415.1_g000001 Rmu_sc0000499.1_g000003 Rmu_sc0000594.1_g000020 Rmu_sc0000673.1_g000007 Rmu_sc0000908.1_g000004 Rmu_sc0001123.1_g000013 Rmu_sc0001123.1_g000014 Rmu_sc0001167.1_g000026 Rmu_sc0001598.1_g000011 Rmu_sc0001696.1_g000003 Rmu_sc0001696.1_g000011 Rmu_sc0001696.1_g000019 Rmu_sc0001696.1_g000020 Rmu_sc0003007.1_g000016 Rmu_sc0003007.1_g000029 Rmu_sc0003051.1_g000010 Rmu_sc0003396.1_g000029 Rmu_sc0004798.1_g000020 Rmu_sc0005375.1_g000016 Rmu_sc0005375.1_g000017 Rmu_sc0005659.1_g000033 Rmu_sc0005659.1_g000034 Rmu_sc0006311.1_g000011 Rmu_sc0008249.1_g000002 Rmu_sc0008249.1_g000018 Rmu_sc0008600.1_g000014 Rmu_sc0009365.1_g000010 Rmu_sc0009365.1_g000022 Rmu_sc0009365.1_g000025 Rmu_sc0011112.1_g000008 Rmu_sc0011112.1_g000009 Rmu_sc0012031.1_g000020 Rmu_sc0013350.1_g000014 Rmu_sc0020359.1_g000004 Rmu_sc0021997.1_g000003 Rmu_sc0021997.1_g000004 Rmu_sc0023610.1_g000002 Rmu_sc0023611.1_g000001 Rmu_sc0028894.1_g000001 Rmu_sc0031050.1_g000001 Rmu_sc0041109.1_g000001 Rmu_ssc0000087.1_g000050 Rmu_ssc0000087.1_g000051 Rmu_ssc0000087.1_g000052 Rmu_ssc0000295.1_g000058 Rmu_ssc0000343.1_g000031 Rmu_ssc0000423.1_g000015 Rmu_ssc0000470.1_g000005 Rmu_ssc0000470.1_g000006
rosa_roxburghii Rroxscaffold_1G00005900 Rroxscaffold_1G00005910 Rroxscaffold_1G00012600 Rroxscaffold_1G00016860 Rroxscaffold_1G00032110 Rroxscaffold_1G00038140 Rroxscaffold_1G00038200 Rroxscaffold_1G00039020 Rroxscaffold_1G00039030 Rroxscaffold_1G00039080 Rroxscaffold_1G00039090 Rroxscaffold_1G00039270 Rroxscaffold_2G00097120 Rroxscaffold_2G00097130 Rroxscaffold_2G00137700 Rroxscaffold_2G00151740 Rroxscaffold_2G00151750 Rroxscaffold_3G00224160 Rroxscaffold_3G00224170 Rroxscaffold_3G00226080 Rroxscaffold_3G00226090 Rroxscaffold_3G00229350 Rroxscaffold_3G00231340 Rroxscaffold_4G00291390 Rroxscaffold_4G00316220 Rroxscaffold_4G00316230 Rroxscaffold_4G00320040 Rroxscaffold_4G00320050 Rroxscaffold_4G00320120 Rroxscaffold_4G00320140 Rroxscaffold_4G00320180 Rroxscaffold_4G00320270 Rroxscaffold_4G00320280 Rroxscaffold_4G00320290 Rroxscaffold_4G00320430 Rroxscaffold_4G00321910 Rroxscaffold_5G00348730 Rroxscaffold_5G00355020 Rroxscaffold_5G00355080 Rroxscaffold_5G00357490 Rroxscaffold_5G00376500 Rroxscaffold_5G00376510 Rroxscaffold_7G00179590 Rroxscaffold_7G00179600 Rroxscaffold_7G00198610
rosa_rugosa Rorug01G0085400 Rorug01G0085400 Rorug01G0085400 Rorug01G0085400 Rorug01G0085400 Rorug01G0085400 Rorug01G0086300 Rorug01G0086500 Rorug01G0087000 Rorug01G0087100 Rorug01G0087600 Rorug01G0087700 Rorug01G0087800 Rorug01G0087800 Rorug01G0302500 Rorug02G0249300 Rorug02G0249300 Rorug02G0249400 Rorug03G0189000 Rorug04G0181800 Rorug04G0283800.1 Rorug04G0283900.1 Rorug05G0043500 Rorug05G0191800 Rorug05G0191900 Rorug05G0192800 Rorug05G0192900 Rorug05G0193000 Rorug05G0201000 Rorug05G0201100 Rorug06G0173900 Rorug06G0173900 Rorug07G0009800 Rorug07G0246300.1 Rorug07G0246400
rosa_samantha Rh1AG103600 Rh1AG104800 Rh1AG105200 Rh1AG105300 Rh1AG105500 Rh1BG082000 Rh1BG082200 Rh1BG082300 Rh1BG082900 Rh1BG083000 Rh1BG083300 Rh1BG083500 Rh1BG083600 Rh1BG083800 Rh1BG083900 Rh1BG084000 Rh1BG084100 Rh1BG084200 Rh1BG092200 Rh1BG275300 Rh1CG098700 Rh1CG098800 Rh1CG100300 Rh1CG100400 Rh1CG100600 Rh1CG100900 Rh1CG101000 Rh1CG101700 Rh1DG066900 Rh1DG067000 Rh1DG106000 Rh1DG107600 Rh1DG107800 Rh1DG108100 Rh1DG108200 Rh1DG108600 Rh1DG108700 Rh1DG108900 Rh1DG109000 Rh1DG109100 Rh1DG109300 Rh1DG109400 Rh1DG109500 Rh1DG109700 Rh1DG109800 Rh1DG173900 Rh2AG270300 Rh2AG398900 Rh2CG245000 Rh2CG260700 Rh2CG278600 Rh2CG342400 Rh2CG385700 Rh3DG197200 Rh3DG197300 Rh4AG015100 Rh4BG347400 Rh4DG360400 Rh5AG278600 Rh5AG278700 Rh5AG286900 Rh5AG287000 Rh5BG282900 Rh5BG283000 Rh5BG283100 Rh5BG291400 Rh5CG314900 Rh5CG315100 Rh5CG315400 Rh5CG315700 Rh5CG315900 Rh5CG316000 Rh5CG323600 Rh5CG323700 Rh5DG291400 Rh5DG292300 Rh5DG292500 Rh5DG292700 Rh5DG292800 Rh5DG292900 Rh5DG301100 Rh5DG301200 Rh5DG301400 Rh5DG350900 Rh6BG407700 Rh6CG294900 Rh6DG286900 Rh7AG400400 Rh7AG420600 Rh7BG381700 Rh7BG395000 Rh7CG418600 Rh7CG440700 Rh7DG396500 Rh7DG413200
rosa_wichuraiana Rw1G003300 Rw1G008240 Rw1G008250 Rw1G008270 Rw1G008330 Rw1G008340 Rw1G008350 Rw1G008360 Rw1G008370 Rw1G008810 Rw1G021140 Rw3G020650 Rw5G026150 Rw5G026200 Rw5G026240 Rw5G026250 Rw5G026650 Rw5G030820 Rw7G006630 Rw7G030060 Rw7G034700

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 307
AciI CCGC 1 cut(s) 139
AcsI RAATTY 1 cut(s) 238
AcuI CTGAAG 1 cut(s) 267
AfaI GTAC 1 cut(s) 263
AfiI CCNNNNNNNGG 2 cut(s) 54, 330
AluBI AGCT 2 cut(s) 66, 151
AluI AGCT 2 cut(s) 66, 151
Alw21I GWGCWC 2 cut(s) 68, 153
Alw26I GTCTC 1 cut(s) 55
ApoI RAATTY 1 cut(s) 238
BanII GRGCYC 2 cut(s) 68, 153
Bbv12I GWGCWC 2 cut(s) 68, 153
BciVI GTATCC 1 cut(s) 124
BcoDI GTCTC 1 cut(s) 55
BfuI GTATCC 1 cut(s) 124
BmsI GCATC 1 cut(s) 268
BpuEI CTTGAG 1 cut(s) 137
BsaJI CCNNGG 2 cut(s) 221, 329
Bsc4I CCNNNNNNNGG 2 cut(s) 54, 330
Bse1I ACTGG 1 cut(s) 293
BseDI CCNNGG 2 cut(s) 221, 329
BseLI CCNNNNNNNGG 2 cut(s) 54, 330
BseMII CTCAG 1 cut(s) 138
BseNI ACTGG 1 cut(s) 293
BsiHKAI GWGCWC 2 cut(s) 68, 153
BslI CCNNNNNNNGG 2 cut(s) 54, 330
BsmAI GTCTC 1 cut(s) 55
BsmBI CGTCTC 1 cut(s) 55
Bsp1286I GDGCHC 2 cut(s) 68, 153
Bsp143I GATC 1 cut(s) 90
BspACI CCGC 1 cut(s) 139
BspCNI CTCAG 1 cut(s) 139
BsrI ACTGG 1 cut(s) 293
BssECI CCNNGG 2 cut(s) 221, 329
BssMI GATC 1 cut(s) 90
BssT1I CCWWGG 2 cut(s) 221, 329
Bst4CI ACNGT 1 cut(s) 187
Bst6I CTCTTC 1 cut(s) 93
BstC8I GCNNGC 1 cut(s) 316
BstDEI CTNAG 1 cut(s) 147
BstKTI GATC 1 cut(s) 93
BstMAI GTCTC 1 cut(s) 55
BstMBI GATC 1 cut(s) 90
BstMWI GCNNNNNNNGC 1 cut(s) 168
BstNSI RCATGY 1 cut(s) 219
BstXI CCANNNNNNTGG 1 cut(s) 300
BsuI GTATCC 1 cut(s) 124
Cac8I GCNNGC 1 cut(s) 316
Csp6I GTAC 1 cut(s) 262
CviAII CATG 2 cut(s) 216, 259
CviJI RGCY 4 cut(s) 66, 151, 162, 269
CviKI_1 RGCY 4 cut(s) 66, 151, 162, 269
CviQI GTAC 1 cut(s) 262
DdeI CTNAG 1 cut(s) 147
DpnI GATC 1 cut(s) 92
DpnII GATC 1 cut(s) 90
Eam1104I CTCTTC 1 cut(s) 93
EarI CTCTTC 1 cut(s) 93
Ecl136II GAGCTC 2 cut(s) 66, 151
Eco130I CCWWGG 2 cut(s) 221, 329
Eco24I GRGCYC 2 cut(s) 68, 153
Eco53kI GAGCTC 2 cut(s) 66, 151
Eco57I CTGAAG 1 cut(s) 267
EcoICRI GAGCTC 2 cut(s) 66, 151
EcoT14I CCWWGG 2 cut(s) 221, 329
EcoT38I GRGCYC 2 cut(s) 68, 153
ErhI CCWWGG 2 cut(s) 221, 329
Esp3I CGTCTC 1 cut(s) 55
FaeI CATG 2 cut(s) 219, 262
FaiI YATR 5 cut(s) 128, 130, 217, 229, 260
FatI CATG 2 cut(s) 215, 258
FauNDI CATATG 1 cut(s) 128
FblI GTMKAC 1 cut(s) 307
FriOI GRGCYC 2 cut(s) 68, 153
Hin1II CATG 2 cut(s) 219, 262
Hpy166II GTNNAC 1 cut(s) 308
Hpy188I TCNGA 4 cut(s) 27, 118, 148, 175
Hpy188III TCNNGA 2 cut(s) 154, 285
Hpy8I GTNNAC 1 cut(s) 308
Hpy99I CGWCG 1 cut(s) 191
HpyAV CCTTC 1 cut(s) 97
HpyCH4III ACNGT 1 cut(s) 187
HpyCH4V TGCA 2 cut(s) 215, 275
HpyF10VI GCNNNNNNNGC 1 cut(s) 168
HpyF3I CTNAG 1 cut(s) 147
Hsp92II CATG 2 cut(s) 219, 262
Kzo9I GATC 1 cut(s) 90
LmnI GCTCC 2 cut(s) 63, 248
LpnPI CCDG 4 cut(s) 39, 256, 270, 306
LweI GCATC 1 cut(s) 268
MalI GATC 1 cut(s) 92
MboI GATC 1 cut(s) 90
MboII GAAGA 3 cut(s) 100, 110, 119
MhlI GDGCHC 2 cut(s) 68, 153
MluCI AATT 2 cut(s) 166, 238
MmeI TCCRAC 1 cut(s) 141
MseI TTAA 2 cut(s) 198, 335
MslI CAYNNNNRTG 1 cut(s) 127
MwoI GCNNNNNNNGC 1 cut(s) 168
NdeI CATATG 1 cut(s) 128
NdeII GATC 1 cut(s) 90
NlaIII CATG 2 cut(s) 219, 262
NspI RCATGY 1 cut(s) 219
Psp124BI GAGCTC 2 cut(s) 68, 153
RsaI GTAC 1 cut(s) 263
RsaNI GTAC 1 cut(s) 262
RseI CAYNNNNRTG 1 cut(s) 127
SacI GAGCTC 2 cut(s) 68, 153
SaqAI TTAA 2 cut(s) 198, 335
Sau3AI GATC 1 cut(s) 90
SduI GDGCHC 2 cut(s) 68, 153
SetI ASST 4 cut(s) 68, 153, 227, 326
SfaNI GCATC 1 cut(s) 268
SmiMI CAYNNNNRTG 1 cut(s) 127
SmlI CTYRAG 1 cut(s) 152
SmoI CTYRAG 1 cut(s) 152
Sse9I AATT 2 cut(s) 166, 238
SsiI CCGC 1 cut(s) 139
SstI GAGCTC 2 cut(s) 68, 153
StyI CCWWGG 2 cut(s) 221, 329
TaaI ACNGT 1 cut(s) 187
TasI AATT 2 cut(s) 166, 238
TatI WGTACW 1 cut(s) 261
Tru1I TTAA 2 cut(s) 198, 335
Tru9I TTAA 2 cut(s) 198, 335
TspDTI ATGAA 3 cut(s) 101, 115, 249
TspGWI ACGGA 1 cut(s) 37
XapI RAATTY 1 cut(s) 238
XceI RCATGY 1 cut(s) 219
XmiI GTMKAC 1 cut(s) 307
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.